Hard to say if I am honest. I think that is what makes LM special. It doesn't fit in a standard genre. I'm not sure what it is. I view Zelda as adventure. LM is more action/horror/puzzle. I lean mostly towards puzzle than anything. For me LM isn't the same genre as Zelda. Granted Zelda is always puzzle heavy. I find genres hard to define in modern gaming. Pikmin is one of my favorites as well, again not sure what genre that is. Resource management?
Pikmin is pretty well defined, RTS, real time strategy. Generally Zelda and LM are both considered Action-Adventure.
You realise you're arguing against opinions right? :P
I definitely wouldn't put Zelda in the same genre as Luigi's Mansion, nor would I lump Pikmin into a general RTS genre. Both those games were pretty much unique when they came out.
As for the topic, difficult question, as the apex is a tall order for a hidden gem. Not sure if it would qualify, but for me, Celeste not only has great gameplay, but the way the story intertwines with the platforming is amazing. It was critically very wel received, but only sold roughly 1 million as far as I can find.